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Open Access Highly Accessed Research article

Genome-wide analysis of WRKY gene family in Cucumis sativus

Jian Ling, Weijie Jiang*, Ying Zhang, Hongjun Yu, Zhenchuan Mao, Xingfang Gu, Sanwen Huang and Bingyan Xie*

Author Affiliations

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China

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BMC Genomics 2011, 12:471  doi:10.1186/1471-2164-12-471

Published: 28 September 2011

Additional files

Additional file 1:

A rooted phylogenetic tree representing relationships among WRKY domains of rice, cucumber and Arabidopsis. The amino acid sequences of the WRKY domain of rice WRKY (OsWRKY), CsWRKY and AtWRKY proteins were used to reconstruct a phylogenetic tree. The most primitive Giardia lamblia WRKY C-terminal domain (GlWRKY1C) was used as an outgroup. Group 1 proteins with the suffix 'N' or 'C' indicates the N-terminal WRKY domains or the C-terminal WRKY domains. Stars and black lines represent orthologous WRKY of cucumber and Arabidopsis. The tree was constructed by PHYLIP 3.2 and displayed by njplot software.

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Additional file 2:

putative orthologs of cucumber and Arabidopsis. Identified WRKY proteins in cucumber and their putative orthologs in Arabidopsis based on phylogenetic studies of WRKY domain sequences.

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Additional file 3:

Amino acid motif analysis of CsWRKY proteins from different groups (or subgroups) and selected group 3 AtWRKY proteins. Motif analysis was performed using Meme 4.0 software. The schematic diagram was obtained by Perl-SVG script and edited in photoshop 7.0.

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Additional file 4:

The schematic diagram of motifs of WRKY proteins. The schematic diagram was deserved from Meme 4.0 software. The order of motifs of WRKY proteins in the diagram was automatically generated by Meme software according to scores.

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Additional file 5:

Comparison of expression pattern of orthologous WRKY pairs under various abiotic stresses. Available expression data on AtWRKY genes from microarray analysis and that of CsWRKY genes generated by real-time PCR analysis were compared.

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Additional file 6:

The expression data for calculating the correlation of orthologs under abiotic stresses. Expression data of Arabidopsis from microarray and of cucumber from Real-time RT-PCR analysis were used to calculate the Pearson correlation of the expression of orthologous WRKY genes pairs under various abiotic stress (at 0, 0.5, 1, 3, 6, 12 and 24 h treatment).

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Additional file 7:

The GenBank accession numbers of WRKY protein sequences used in the manuscript. GenBank accession numbers of WRKY protein were from NCBI or PFAM database.

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Additional file 8:

The primer sequences used for RT-PCR amplification of 48 CsWRKY genes. The specific primers were designed according to the WRKY gene sequences by Primer 5 software.

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Additional file 9:

The primer sequences used for real-time PCR of stress-responsive and group 3 CsWRKY genes. The specific primers were designed according to the WRKY gene sequences by Primer 5 software.

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Additional file 10:

The expression patterns of stress-inducible CsWRKY genes were shown by real-time PCR analyses under three different abiotic stresses. Expression of stress-inducible CsWRKY genes were shown by real-time PCR analyses under three different abiotic stresses. The pictures of the first column, the second column and the third column indicated the expression pattern under cold treatment, drought treatment and salt treatment respectively. For each picture, the y-axis indicated the relative fold of treatment to control and x-axis indicate the time under treatment. (A),CsWRKY2; (B),CsWRKY18; (C),CsWRKY21; (D),CsWRKY40; (E),CsWRKY46. This is the originally pictures produced by Bio-Rad CFX manager software automatically.

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Additional file 11:

The Ct-values and standard deviation for the real time RT-PCR of CsWRKY genes. The Ct-value and standard deviation of CsWRKY genes and their corresponding actin control under different treatments.

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